Synthetic Associations Created by Rare Variants Do Not Explain Most GWAS Results
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For a disease with 80% heritability, theory indicates the number of contributing loci ranges from over 500 with GRR 2 and one very rare variant per locus to about a dozen loci with GRR 5 and allele frequencies of 1% if the disease is common.
“For a disease with a high heritability of 80%, theory indicates that the number of contributing loci can range from over 500 with GRR of just 2 and one very rare variant per locus, to just a dozen loci with GRR of 5 and allele frequencies of 1% or if the disease is relatively common19.”
From Rare and common variants: twenty arguments (2012) · cites this paper as [19]
Analysis of allele frequency distributions in GWAS data is a major argument against rare variants as the predominant source of missing heritability.
“A major argument against rare variants as the predominant source of missing heritability comes from the analysis of allele frequency distributions of GWAS data19.”
From Rare and common variants: twenty arguments (2012) · cites this paper as [19]
Synthetic association is not expected to account for most missing heritability.
“Synthetic association is not expected to account for most of the missing heritability19, 51”
From Rare and common variants: twenty arguments (2012) · cites this paper as [19]
Linkage disequilibrium considerations using standard quantitative genetic theory place strong constraints on the number and effect-size range of rare variants that could make a major contribution yet remain undetected in GWAS.
“considerations of linkage disequilibrium using standard quantitative genetic theory19 place strong constraints on the number of rare variants and their range of effect sizes that would be compatible with them making a major contribution yet remaining undetected in GWAS”
From Rare and common variants: twenty arguments (2012) · cites this paper as [19]
The Procrustean theory that common variant signals inevitably reflect "synthetic associations" to rare, high penetrance mutations is not credible.
“The Procrustean theory that common variant signals inevitably reflect “synthetic associations” 124 to rare, high penetrance mutations is not credible. 77,125–127”
From Genetic architectures of psychiatric disorders: the emerging picture and its implications (2012) · cites this paper as [126]
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- Authors
- Wray, N. R., Purcell, S. M., & Visscher, P. M.
- Affiliations
- QIMR Berghofer Medical Research Institute (AU)
- Broad Institute (US)
- Corresponding author
- Wray, Naomi R.
- Venue
- PLoS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2011-01-18
- Volume
- 9
- Issue
- 1
- Pages
- e1000579
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- PMC
- PMC3022526
- OpenAlex
- W2160362734
- Cited by
- 176
- References
- 23
- Citations by year
- 2026: 12 · 2025: 3 · 2024: 7 · 2023: 3 · 2022: 2 · 2021: 7 · 2020: 3 · 2019: 6 · 2018: 3 · 2017: 8 · 2016: 17 · 2015: 19 · 2014: 18 · 2013: 22 · 2012: 33
- FWCI
- 17.16
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Goddard Space Flight Center
- Medical Research Council
- Australian Research Council (DP1093900, DP0770096)
- National Health and Medical Research Council (613601, 613672, 496688, 442915, DP0770096, 389892)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Keywords
- rare variants, genome-wide association study
- MeSH terms
- Computer Simulation, Humans, Models, Genetic, Schizophrenia, Genetic Variation, Linkage Disequilibrium, Multifactorial Inheritance, Genome-Wide Association Study, Genetic Loci
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